chr1-85278058-G-T

Variant names:

• chr1-85278058-G-T
• rs2735592
• ENST00000791167.1:n.627G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_045484.1(BCL10-AS1):​n.858G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,052 control chromosomes in the GnomAD database, including 40,334 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.73 (40334 hom., cov: 32)
• Consequence: BCL10-AS1 NR_045484.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 17 publications found

Genes affected

BCL10-AS1 (HGNC:55868): (BCL10 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_045484.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL10-AS1	NR_045484.1		n.858G>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL10-AS1	ENST00000791167.1		n.627G>T		non_coding_transcript_exon	Exon 2 of 2
	BCL10-AS1	ENST00000426125.1	TSL:3	n.67+320G>T		intron	N/A
	BCL10-AS1	ENST00000427819.5	TSL:2	n.181+320G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110366 AN: 151934 Hom.: 40303 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.712

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.726 AC: 110445 AN: 152052 Hom.: 40334 Cov.: 32 AF XY: 0.726 AC XY: 53993 AN XY: 74328

African (AFR) AF: 0.785 AC: 32554 AN: 41468

American (AMR) AF: 0.683 AC: 10437 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3617 AN: 5174

South Asian (SAS) AF: 0.733 AC: 3529 AN: 4814

European-Finnish (FIN) AF: 0.721 AC: 7613 AN: 10552

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47929 AN: 67972

Other (OTH) AF: 0.716 AC: 1512 AN: 2112

Alfa AF: 0.710 Hom.: 60200

Bravo AF: 0.725

Asia WGS AF: 0.747 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.56
PhyloP100		0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2735592; hg19: chr1-85743741;